Analyses Of Chloroplast DNA Sequences Research Articles

Riccardiothallus devonicus gen. et sp. nov., the earliest simple thalloid liverwort from the Lower Devonian of Yunnan, China

This paper describes a fossil liverwort in the Posongchong Formation, Lower Devonian (Pragian), Yunnan, China preserved as a partially permineralized compression in gray arenaceous mudstone. The plant comprises a regularly-bifurcating flat ecostate multilayered thallus with entire margins. Following comparisons of this fossil with gametophytes of extant and fossil liverworts, a new genus Riccardiothallus was established in the family Aneuraceae (Jungermanniopsida). The fossil, which appears to be closely similar to several members of the extant genus Riccardia, is the earliest unequivocal megafossil evidence of a liverwort. Considering the sedimentary environment of Riccardiothallus devonicus and the habitats of many extant Riccardia species, we conclude that Riccardiothallus devonicus probably lived in a warm and humid riverine environment. The age (Pragian, 407–411Ma) of Riccardiothallus devonicus suggests that the differentiation of Jungermanniopsida and Metzgeriidae was in the Early Devonian, significantly earlier than the assumptions derived from analyses of chloroplast DNA sequences of modern liverworts and current total evidence phylogenies (Late Devonian, 359–385Ma; Late Carboniferous, 299–307Ma).

<p class="HeadingRunIn"><strong><em>Navarretia furnissii</em> (Polemoniaceae), a new diploid species from the intermountain western United States distinguished from tetraploid <em>Navarretia saximontana</em></strong></p>

Morphological and DNA-based characters distinguish a new diploid species centered in the Intermountain Region of the western United States, Navarretia furnissii, from N. saximontana, which is tetraploid. The two species are reciprocally monophyletic in analyses of chloroplast DNA sequences and nrDNA ITS sequences. Navarretia furnissii, presently known from Utah, Idaho, Wyoming, Montana, and Colorado, is distinguished morphologically from N. saximontana by a smaller corolla, greater frequency of pronged calyx lobes, and fewer seeds. A key to Navarretia of the Intermountain Region is presented.

The Relationship Between Anisosperma and Fevillea (Cucurbitaceae), and a New Species of Fevillea from Bolivia

Abstract We describe and illustrate the new species Fevillea anomalosperma from the semideciduous forests of northwestern Bolivia. Analysis of chloroplast DNA sequences representing most genera of Cucurbitaceae, including Fevillea with four of its seven species, supports placing the new species in Fevillea despite its small (10–11.5 × 7.5–10 mm, 2–3 mm thick), flattened, and highly sculptured seeds, which are unusual in the genus. The molecular phylogeny also revealed that the recent sinking of the monotypic genus Anisosperma into Fevillea is not justified.

DNA Polymorphisms Reveal Geographic Races of Reed Canarygrass

ABSTRACTReed canarygrass (Phalaris arundinacea L.) is a cool‐season perennial with a circumglobal distribution in the northern hemisphere, native to Europe, Asia, and North America. Repeated introductions of European germplasm into North America have created confusion over the origins of reed canarygrass germplasm found in wetlands, pastures, and breeding programs. The objectives of this study were to identify sources of DNA marker variation among reed canarygrass cultivars from Europe and North America and between landraces and improved cultivars from North America. Analysis of 205 reed canarygrass plants from 15 cultivars based on 102 amplified fragment length polymorphic (AFLP) DNA markers revealed two groups of cultivars. One group consisted of three closely related but geographically diverse North American landraces that were completely separated from all other plants in only two dimensions of the AFLP incidence matrix. The complete discrimination of these plants from all European plants suggests their possible origin from native North American germplasm. These results were supported by chloroplast DNA sequence analysis, which additionally revealed separation of a potential Scandinavian cytoplasmic race from the continental European cytoplasmic race. This is the strongest evidence to date suggesting that native North American reed canarygrass germplasm has been preserved within cultivars of this species.

Multiple introductions are responsible for the disjunct distributions of invasive Parthenium hysterophorus in China: evidence from nuclear and chloroplast DNA

Summary Parthenium hysterophorus is an invasive weed native to tropical and subtropical America. Since its introduction into China in 1926, this weed has been limited to southern areas (18°–25°N). However, new populations were recently reported in Shandong (35°N). The origin of this geographically isolated population remains unclear. In this study, we used inter simple sequence repeat and chloroplast DNA sequence markers (trnQ‐5’rps16) to investigate the genetic structure of 18 invading populations of P. hysterophorus and to examine the genetic relationship of Shandong and southern populations. Our data show that Shandong population is genetically different and has apparently higher levels of genetic diversity than most populations in southern China. Both neighbour‐joining clustering and principal coordination analysis clearly separated Shandong from other populations. Chloroplast DNA sequence analysis further confirmed that the Shandong population was characterised by a unique haplotype that was not found in southern populations. We conclude that the population in Shandong may have been independently introduced from areas outside China. As P. hysterophorus has a broad potential distribution in China, attention should be paid to both international and domestic quarantine to prevent new introductions and curtail the possible hybridisation and gene flow between populations in different regions.

Species relationships and genetic variation in the New Zealand endemic Leucogenes (Asteraceae: Gnaphalieae)

AFLP profiles, nuclear ITS sequences, and chloroplast psbA-trnH intergenic spacer sequences for representative samples of the New Zealand edelweiss species Leucogenes grandiceps, L. leontopodium, L. neglecta, and L. tarahaoa were examined. Analysis of AFLP profiles from a small number of populations strongly groups samples of each species, and in turn samples of diploid (2n = 2x = 28) L. leontopodium and tetraploid (2n = 4x = 56) L. neglecta cluster together, consistent with a derivation of the latter from the former by auto‐polyploidy. However, octoploid (2n = 8x = 112) L. tarahaoa does not cluster closely with either L. neglecta or L. leontopodium, indicating this species has an independent origin. Analyses of chloroplast DNA sequences show that although the majority of Leucogenes samples share similar chloroplast sequences not sampled from other species of New Zealand Gnaphalieae, a single accession of L. grandiceps and North island populations of L. leontopodium share chloroplast sequences more similar to other species of New Zealand Gnaphalieae. ITS sequence variation is more complex, with sequences sampled from Leucogenes not constituting a monophyletic group, and striking intraspecific variation detected within L. grandiceps.

Mitochondrial sequence data and Dipsacales phylogeny: Mixed models, partitioned Bayesian analyses, and model selection

Phylogenetic analyses of chloroplast DNA sequences, morphology, and combined data have provided consistent support for many of the major branches within the angiosperm clade Dipsacales. Here we use sequences from three mitochondrial loci to test the existing broad scale phylogeny and in an attempt to resolve several relationships that have remained uncertain. Parsimony, maximum likelihood, and Bayesian analyses of a combined mitochondrial data set recover trees broadly consistent with previous studies, although resolution and support are lower than in the largest chloroplast analyses. Combining chloroplast and mitochondrial data results in a generally well-resolved and very strongly supported topology but the previously recognized problem areas remain. To investigate why these relationships have been difficult to resolve we conducted a series of experiments using different data partitions and heterogeneous substitution models. Usually more complex modeling schemes are favored regardless of the partitions recognized but model choice had little effect on topology or support values. In contrast there are consistent but weakly supported differences in the topologies recovered from coding and non-coding matrices. These conflicts directly correspond to relationships that were poorly resolved in analyses of the full combined chloroplast–mitochondrial data set. We suggest incongruent signal has contributed to our inability to confidently resolve these problem areas.

Central Asian origin of and strong genetic differentiation among populations of the rare and disjunct Carex atrofusca (Cyperaceae) in the Alps

AbstractAim Carex atrofusca has an arctic–alpine distribution in the Northern Hemisphere, with only a few, disjunct localities known in the European Alps. These alpine populations are declining in number and size. In contrast, C. atrofusca has a wide circumpolar distribution range and is abundant in large parts of the Arctic. The degree of genetic differentiation of the alpine populations and their importance for the conservation of the intraspecific genetic variation of the species is unknown.Location Eurasia and Greenland, with emphasis on the European Alps.Methods We applied amplified fragment length polymorphism (AFLP) fingerprinting and sequences of chloroplast DNA to determine the position of the alpine populations in a circumpolar phylogeography of C. atrofusca and to unravel the patterns of genetic diversity and differentiation within the Alps.Results Two distinct major groups were detected in a neighbour‐joining analysis of AFLP data and in parsimony analysis of chloroplast DNA sequences: one consisting of the populations from Siberia and Greenland and one consisting of all European populations as sister to the populations from Central Asia. Within Europe, the populations from the Tatra Mountains and those from Scotland and Scandinavia formed two well‐supported groups, whereas the alpine populations did not constitute a group of their own. The genetic variation in the Alps was almost completely partitioned among the populations, and the populations were almost invariable.Main conclusions The alpine populations possibly originated due to immigration from Central Asia. The strong differentiation among them suggests that genetic drift has been strongly acting on the populations, either as a consequence of founder events during colonization or due to subsequent reduction of population sizes during warm stages of the Holocene.

Evidences for multiple maternal lineages of Caryocar brasiliense populations in the Brazilian Cerrado based on the analysis of chloroplast DNA sequences and microsatellite haplotype variation.

In this work we report on the phylogeography of the endangered tree species Caryocar brasiliense based on variability in two classes of maternally inherited chloroplast DNA sequences with different rates of molecular evolution. Eleven sequence haplotypes of a noncoding region between the genes trnT and trnF and 21 distinct 10-locus microsatellite haplotypes could be identified in a total of 160 individuals, collected in 10 widespread populations of C. brasiliense. An amova indicated that most of the variation can be attributed to differences among populations, both for DNA sequence (87.51%) and microsatellites (84.38%). Phylogeography based on a median-joining network analysis of the noncoding region showed a sharp difference from the analysis of microsatellite haplotypes. Nevertheless, both analyses indicated that multiple lineages may have contributed to the origin of C. brasiliense populations in Brazilian Cerrado. Incongruences in the microsatellite haplotypes network suggest that homoplasy, which emerged from recurrent and independent mutations, greatly influenced the evolution of the C. brasiliense chloroplast genome. We hypothesize that our results may show the outcome of the restriction of ancient relic populations to moist refugias during extended droughts coinciding with glaciation in the northern hemisphere. The subsequent spread to favourable areas throughout Central Brazil may have caused contact between different lineages during the interglacial periods. The extinction of megafauna dispersers in the last glaciation may have caused a restriction in seed movement and currently, gene flow has been occurring mainly by pollen movement.

Origin of Triploids of Elatostema suzukii (Urticaceae) on Okinawa Island, the Ryukyus

, an endemic species occurring only along streams in the Yanbaru area in the north of Okinawa Island, the Ryukyus, is known to comprise di-, tri-, and tetraploids with x=13. Molecular analysis of chloroplast DNA sequences has shown that two haplotypes, AT- and NI-types, characterized by the insertion or deletion of four nucleotides “ATAT”, exist in E. suzukii. The AT-type was found in some diploids and triploids only at Genkagawa, whereas the NI-type is widespread, occurring in both diploids and triploids of the Genkagawa site as well as at other localities. The triploids share both types with the diploids, indicating that the triploids have at least two independent origins. Because of its restricted distribution, the AT-type triploid may have arisen within the Genkagawa area.

Chemotaxonomy of Plantago. Iridoid glucosides and caffeoyl phenylethanoid glycosides

Data for 34 species of Plantago (Plantaginaceae), including subgen. Littorella (= Littorella uniflora), have been collected with regard to their content of iridoid glucosides and caffeoyl phenylethanoid glycosides (CPGs). In the present work, 21 species were investigated for the first time and many known compounds were found together with three new iridoid glucosides. Of these, arborescoside and arborescosidic acid, both of the uncommon type with an 8,9-double bond, were present in several species, while 6-deoxymelittoside was found only in P. subulata. The known compounds deoxyloganic acid, caryoptoside and rehmannioside D were isolated from the genus for the first time. The earlier reported occurrence of sorbitol in the family was confirmed, and this compound was shown by NMR spectroscopy to be the main sugar in the three species investigated for this. The combined data show that CPGs are present in all species investigated. With regard to the iridoids, the distribution patterns showed a good correlation with the classification of Rahn. Thus, aucubin is typical for the whole genus, while bartsioside and catalpol as well as 5-substituted iridoids are each characteristic for a subgenus in the family. Finally, the close relationship between Plantago and Veronica suggested by chloroplast DNA sequence analysis, could be corroborated by the common occurrence of the rare 8,9-unsaturated iridoids in these two genera.

Genetic diversity in Mexican Stylosanthes humilis as revealed by AFLP, compared to the variability S. humilis accessions of South American origin

Amplified fragment length polymorphism (AFLP) analysis was used to determine genetic relationships among 32 accessions of the species Stylosanthes humilis, representing 26 and 6 accessions of Mexican and South American origin, respectively. Seven AFLP primer pairs generated a total of 111 polymorphic bands with an average of 15.8 polymorphisms per combination and a polymorphic information content ranging from 0.89 to 0.79. Cluster analysis and principal coordinates analysis of the calculated similarity matrix clearly separated all the Mexican accessions, with one exception, from the accessions of South American origin. The observation of differentiation of these two main groups by AFLP analysis is highly congruent with previous studies based on morphological descriptors, cross-hybridization experiments, and chloroplast DNA sequence analysis, and may suggest that both groups evolved separately due to geographical isolation in the past, resulting in the existence of at least 2 principal gene pools. Within the Mexican collection, three groups were recognized, each corresponding to a geographical region with a low within-group and a high between-group genetic variability. Although most Mexican accessions formed one major group, one accession clustered with the South American gene pool. These findings show that Mexico may contain unique sources of S.humilis and therefore would merit attention for conservation and maintenance of S. humilis germplasm. Also, these results demonstrate that AFLP analysis is an efficient method for assessing genetic diversity among S. humilis accessions.

Evolutionary Analysis of Plant DNA Sequences

The comparative analysis of DNA sequence data reveals much about plant evolution. We have used maximum-likelihood algorithms, based on sequence comparisons for homologous chloroplast-encoded genes, to investigate plant phylogeny. These analyses show that the origin of three subclasses of dicots (represented by pea, spinach, and tobacco) occurred during approximately the same epoch in evolution. It is also possible to extend the phylogenetic analyses to green algae and cyanobacteria, such that virtually the entire spectrum of evolution in the plant kingdom is included. The analyses of chloroplast DNA sequences among higher plants are remarkably consistent, in that different coding and noncoding sequences yield the same phylogenies. This overall consistency is apparent despite different rates of evolution by codon position, differential rates of evolution for some branches of the phylogenetic topologies, and differences in model constraints. We conclude from these analyses that DNA sequence comparisons of c...

Localization and sequence analysis of chloroplast DNA sequences of Chlamydomonas reinhardii that promote autonomous replication in yeast

Four distinct chloroplast DNA segments from Chlamydomonas reinhardii of 400, 415, 730 and 2300 bp which promote autonomous replication in yeast have been mapped on the chloroplast genome. Plasmids carrying these chloroplast DNA fragments are unstable in yeast when the cells are grown under non-selective conditions. Sequence analysis of three of these chloroplast ARS regions (autonomously replicating sequences in yeast) reveals a high AT content, numerous short direct and inverted repeats and the presence of at least one element in each region that is related to the yeast ARS consensus sequence. A/T TTTATPuTTT A/T. These three chloroplast regions share, in addition, two common elements of 10 and 11 bp which may play a role in promoting autonomous replication.